File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3769ms, 79.11% of 4764ms total Dropped 706 nodes (cum <= 23.82ms) flat flat% sum% cum cum% 0 0% 0% 4540ms 95.30% __libc_start_call_main 0 0% 0% 4540ms 95.30% __libc_start_main_impl 0 0% 0% 4540ms 95.30% _start 0 0% 0% 4523ms 94.94% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4523ms 94.94% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4523ms 94.94% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4523ms 94.94% main 0 0% 0% 4489ms 94.23% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4489ms 94.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4489ms 94.23% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4478ms 94.00% AbstractCellBasedSimulation::Solve 0 0% 0% 4218ms 88.54% AbstractCellPopulation::WriteResultsToFiles 10ms 0.21% 0.21% 3988ms 83.71% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.21% 1989ms 41.75% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.23% 1695ms 35.58% VertexMeshWriter::MakeVtkMesh 0 0% 0.23% 1241ms 26.05% vtkPolygon::New 0 0% 0.23% 1238ms 25.99% vtkPolygon::vtkPolygon 10ms 0.21% 0.44% 903ms 18.95% vtkCell::vtkCell 1ms 0.021% 0.46% 772ms 16.20% vtkPoints::New 1ms 0.021% 0.48% 755ms 15.85% VertexMeshWriter::WriteFiles 14ms 0.29% 0.78% 742ms 15.58% vtkPoints::vtkPoints 3ms 0.063% 0.84% 741ms 15.55% std::ostream::operator<< (inline) 51ms 1.07% 1.91% 739ms 15.51% std::ostream::_M_insert 35ms 0.73% 2.64% 671ms 14.08% operator new 209ms 4.39% 7.03% 641ms 13.46% __GI___libc_malloc 48ms 1.01% 8.04% 604ms 12.68% std::num_put::_M_insert_float 0 0% 8.04% 599ms 12.57% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.04% 599ms 12.57% vtkXMLWriterBase::Write 0 0% 8.04% 593ms 12.45% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.04% 593ms 12.45% vtkExecutive::CallAlgorithm 0 0% 8.04% 593ms 12.45% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.04% 591ms 12.41% vtkCompositeDataPipeline::ExecuteData 0 0% 8.04% 591ms 12.41% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.04% 590ms 12.38% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.042% 8.08% 587ms 12.32% vtkQuad::New 0 0% 8.08% 584ms 12.26% vtkLine::New 4ms 0.084% 8.17% 583ms 12.24% vtkQuad::vtkQuad 10ms 0.21% 8.38% 567ms 11.90% vtkLine::vtkLine 182ms 3.82% 12.20% 550ms 11.54% __GI___libc_free 0 0% 12.20% 547ms 11.48% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 12.20% 547ms 11.48% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 12.20% 527ms 11.06% vtkTriangle::New 7ms 0.15% 12.34% 522ms 10.96% vtkTriangle::vtkTriangle 0 0% 12.34% 489ms 10.26% vtkXMLWriter::WriteBinaryData 9ms 0.19% 12.53% 480ms 10.08% std::__cxx11::collate::do_transform 1ms 0.021% 12.55% 479ms 10.05% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.55% 479ms 10.05% vtkXMLWriter::WriteBinaryDataInternal 22ms 0.46% 13.01% 465ms 9.76% vtkPoints::SetDataType 0 0% 13.01% 455ms 9.55% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.021% 13.04% 451ms 9.47% ___vsnprintf 1ms 0.021% 13.06% 450ms 9.45% __vsnprintf_internal (inline) 58ms 1.22% 14.27% 433ms 9.09% __printf_buffer 3ms 0.063% 14.34% 413ms 8.67% vtkPolygon::~vtkPolygon 240ms 5.04% 19.37% 367ms 7.70% _int_free 0 0% 19.37% 346ms 7.26% vtkXMLWriter::WritePointsAppendedData 0 0% 19.37% 345ms 7.24% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 19.37% 343ms 7.20% VtkMeshWriter::WriteFiles 239ms 5.02% 24.39% 343ms 7.20% _int_malloc 1ms 0.021% 24.41% 340ms 7.14% __printf_fp_spec (inline) 14ms 0.29% 24.71% 339ms 7.12% __printf_fp_l_buffer 2ms 0.042% 24.75% 324ms 6.80% vtkCell::~vtkCell 158ms 3.32% 28.06% 310ms 6.51% __printf_fp_buffer_1 32ms 0.67% 28.74% 297ms 6.23% std::__new_allocator::allocate (inline) 0 0% 28.74% 295ms 6.19% std::allocator_traits::allocate (inline) 44ms 0.92% 29.66% 295ms 6.19% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 29.66% 252ms 5.29% OnLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.042% 29.70% 252ms 5.29% PottsBasedCellPopulation::UpdateCellLocations 10ms 0.21% 29.91% 252ms 5.29% vtkBase64OutputStream::Write 2ms 0.042% 29.95% 249ms 5.23% std::__new_allocator::deallocate (inline) 0 0% 29.95% 247ms 5.18% std::allocator_traits::deallocate (inline) 24ms 0.5% 30.46% 242ms 5.08% vtkBase64OutputStream::EncodeTriplet 0 0% 30.46% 228ms 4.79% vtkXMLWriter::WriteCompressionBlock 6ms 0.13% 30.58% 227ms 4.76% vtkPoints::~vtkPoints 0 0% 30.58% 217ms 4.55% vtkDataCompressor::Compress 0 0% 30.58% 216ms 4.53% compress2 0 0% 30.58% 216ms 4.53% vtkZLibDataCompressor::CompressBuffer 56ms 1.18% 31.76% 212ms 4.45% crc32 0 0% 31.76% 212ms 4.45% deflate 80ms 1.68% 33.44% 203ms 4.26% std::ostream::write 4ms 0.084% 33.52% 198ms 4.16% vtkFloatArray::New 0 0% 33.52% 194ms 4.07% tbb::detail::r1::parallel_pipeline 1ms 0.021% 33.54% 187ms 3.93% vtkQuad::~vtkQuad 0 0% 33.54% 186ms 3.90% clone3 0 0% 33.54% 186ms 3.90% start_thread 0 0% 33.54% 184ms 3.86% tbb::detail::r1::reset 75ms 1.57% 35.12% 184ms 3.86% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.063% 35.18% 178ms 3.74% vtkLine::GetParametricCenter 2ms 0.042% 35.22% 169ms 3.55% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 35.22% 168ms 3.53% vtkFloatArray::vtkFloatArray 2ms 0.042% 35.26% 167ms 3.51% vtkTriangle::~vtkTriangle 1ms 0.021% 35.29% 161ms 3.38% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 35.29% 157ms 3.30% std::_Rb_tree::_M_create_node (inline) 0 0% 35.29% 156ms 3.27% NodeLocationWriter::VisitAnyPopulation 1ms 0.021% 35.31% 154ms 3.23% VertexMesh::VertexMesh 9ms 0.19% 35.50% 154ms 3.23% std::vector::_M_default_append 1ms 0.021% 35.52% 153ms 3.21% std::set::set (inline) 4ms 0.084% 35.60% 153ms 3.21% vtkIdList::AllocateInternal 0 0% 35.60% 152ms 3.19% std::_Rb_tree::_M_get_node (inline) 7ms 0.15% 35.75% 152ms 3.19% std::_Rb_tree::_Rb_tree 1ms 0.021% 35.77% 148ms 3.11% std::_Vector_base::_M_deallocate (inline) 1ms 0.021% 35.79% 147ms 3.09% VertexMesh::GenerateEdgesFromElements (inline) 86ms 1.81% 37.59% 146ms 3.06% malloc_consolidate 5ms 0.1% 37.70% 145ms 3.04% MutableElement::BuildEdges 34ms 0.71% 38.41% 144ms 3.02% std::_Rb_tree::_M_erase 1ms 0.021% 38.43% 144ms 3.02% std::_Vector_base::_M_allocate (inline) 5ms 0.1% 38.54% 144ms 3.02% vtkFloatArray::~vtkFloatArray 141ms 2.96% 41.50% 141ms 2.96% [libz.so.1.3] 0 0% 41.50% 138ms 2.90% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.042% 41.54% 138ms 2.90% std::_Rb_tree::~_Rb_tree (inline) 0 0% 41.54% 138ms 2.90% std::vector::~vector (inline) 5ms 0.1% 41.65% 137ms 2.88% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 41.65% 137ms 2.88% VertexMesh::~VertexMesh 2ms 0.042% 41.69% 132ms 2.77% vtkDataArray::CreateDataArray 0 0% 41.69% 131ms 2.75% CellPropertyCollection::GetPropertiesType (inline) 14ms 0.29% 41.98% 130ms 2.73% std::_Rb_tree::_M_copy (inline) 2ms 0.042% 42.02% 128ms 2.69% vtkDoubleArray::vtkDoubleArray 1ms 0.021% 42.04% 127ms 2.67% EdgeHelper::GetEdgeFromNodes 124ms 2.60% 44.65% 124ms 2.60% __strcmp_avx2 8ms 0.17% 44.82% 124ms 2.60% vtkTypeFloat64Array::New 55ms 1.15% 45.97% 122ms 2.56% std::basic_filebuf::xsputn 24ms 0.5% 46.47% 119ms 2.50% vtkObject::vtkObject 0 0% 46.47% 118ms 2.48% std::set::~set (inline) 14ms 0.29% 46.77% 115ms 2.41% std::_Rb_tree::_M_clone_node (inline) 2ms 0.042% 46.81% 110ms 2.31% AbstractCellProperty::IsSubType (inline) 30ms 0.63% 47.44% 108ms 2.27% __dynamic_cast 0 0% 47.44% 108ms 2.27% std::_Vector_base::~_Vector_base (inline) 51ms 1.07% 48.51% 108ms 2.27% std::__ostream_insert 3ms 0.063% 48.57% 108ms 2.27% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.021% 48.59% 107ms 2.25% std::operator<< (inline) 0 0% 48.59% 107ms 2.25% vtkXMLWriter::WritePointDataAppendedData 106ms 2.23% 50.82% 106ms 2.23% __GI_sched_yield 0 0% 50.82% 101ms 2.12% std::_Rb_tree::_M_drop_node (inline) 0 0% 50.82% 99ms 2.08% std::_Rb_tree::_M_put_node (inline) 1ms 0.021% 50.84% 99ms 2.08% vtkIdList::Allocate 46ms 0.97% 51.81% 99ms 2.08% vtkTypeFloat64Array::PrintSelf 1ms 0.021% 51.83% 96ms 2.02% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 69ms 1.45% 53.27% 94ms 1.97% std::basic_streambuf::xsputn 2ms 0.042% 53.32% 94ms 1.97% std::map::operator[] (partial-inline) 0 0% 53.32% 93ms 1.95% EdgeHelper::~EdgeHelper (inline) 0 0% 53.32% 92ms 1.93% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.042% 53.36% 88ms 1.85% std::vector::push_back (inline) 4ms 0.084% 53.44% 85ms 1.78% AbstractCellProperty::IsType (inline) 14ms 0.29% 53.74% 85ms 1.78% vtkAOSDataArrayTemplate::DataElementChanged 23ms 0.48% 54.22% 84ms 1.76% vtkObject::Modified 0 0% 54.22% 83ms 1.74% Cell::HasCellProperty (inline) 2ms 0.042% 54.26% 83ms 1.74% CellPropertyCollection::HasProperty 46ms 0.97% 55.23% 82ms 1.72% hack_digit 51ms 1.07% 56.30% 80ms 1.68% vtkObjectBase::UnRegisterInternal 0 0% 56.30% 78ms 1.64% tcache_get (inline) 78ms 1.64% 57.93% 78ms 1.64% tcache_get_n (inline) 7ms 0.15% 58.08% 77ms 1.62% _int_free_maybe_consolidate 77ms 1.62% 59.70% 77ms 1.62% unlink_chunk 2ms 0.042% 59.74% 76ms 1.60% vtkDoubleArray::~vtkDoubleArray 3ms 0.063% 59.80% 73ms 1.53% vtkIdList::New 9ms 0.19% 59.99% 69ms 1.45% AbstractCellProperty::IsSame 18ms 0.38% 60.37% 68ms 1.43% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.021% 60.39% 67ms 1.41% Cell::GetCellProliferativeType 3ms 0.063% 60.45% 66ms 1.39% std::vector::_M_realloc_insert 10ms 0.21% 60.66% 60ms 1.26% std::type_info::operator== (inline) 60ms 1.26% 61.92% 60ms 1.26% vtkTimeStamp::Modified 8ms 0.17% 62.09% 59ms 1.24% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.084% 62.17% 58ms 1.22% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.13% 62.30% 58ms 1.22% std::num_put::_M_insert_int 1ms 0.021% 62.32% 57ms 1.20% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 22ms 0.46% 62.78% 56ms 1.18% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.042% 62.83% 55ms 1.15% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 62.83% 55ms 1.15% NodesOnlyMesh::SetUpBoxCollection 0 0% 62.83% 54ms 1.13% boost::numeric::ublas::vector_assign (inline) 0 0% 62.83% 53ms 1.11% NodesOnlyMesh::~NodesOnlyMesh 0 0% 62.83% 53ms 1.11% std::_Rb_tree::lower_bound (inline) 0 0% 62.83% 53ms 1.11% std::map::lower_bound (inline) 0 0% 62.83% 53ms 1.11% std::set::insert (inline) 9ms 0.19% 63.01% 53ms 1.11% vtkDataArray::vtkDataArray 1ms 0.021% 63.04% 52ms 1.09% std::_Rb_tree::_M_insert_unique 51ms 1.07% 64.11% 51ms 1.07% __memcpy_avx_unaligned_erms 35ms 0.73% 64.84% 51ms 1.07% std::_Hashtable::clear 10ms 0.21% 65.05% 51ms 1.07% vtkIdList::~vtkIdList 27ms 0.57% 65.62% 49ms 1.03% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 65.62% 49ms 1.03% DistributedBoxCollection::IsOwned 7ms 0.15% 65.76% 49ms 1.03% std::_Rb_tree::_M_insert_ (inline) 0 0% 65.76% 48ms 1.01% std::make_unique (inline) 48ms 1.01% 66.77% 48ms 1.01% std::ostream::sentry::sentry 2ms 0.042% 66.81% 44ms 0.92% VertexMesh::Clear 11ms 0.23% 67.04% 44ms 0.92% boost::numeric::ublas::indexing_vector_assign 8ms 0.17% 67.21% 44ms 0.92% vtkDataArray::~vtkDataArray 6ms 0.13% 67.34% 43ms 0.9% vtkAbstractArray::vtkAbstractArray 0 0% 67.34% 43ms 0.9% vtkDataArray::ComputeRange 41ms 0.86% 68.20% 41ms 0.86% __GI___writev 0 0% 68.20% 41ms 0.86% std::__basic_file::xsputn_2 40ms 0.84% 69.04% 41ms 0.86% vtkObjectBase::Delete 3ms 0.063% 69.10% 40ms 0.84% VertexMeshWriter::GetNextNode 0 0% 69.10% 39ms 0.82% _dl_init 0 0% 69.10% 39ms 0.82% call_init (inline) 3ms 0.063% 69.16% 39ms 0.82% vtkDoubleArray::New 0 0% 69.16% 38ms 0.8% Cell::GetMutationState 2ms 0.042% 69.21% 38ms 0.8% DistributedBoxCollection::SetupLocalBoxesHalfOnly 1ms 0.021% 69.23% 38ms 0.8% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 69.23% 38ms 0.8% _dl_start_user 2ms 0.042% 69.27% 37ms 0.78% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 69.27% 37ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.042% 69.31% 36ms 0.76% Edge::Edge 36ms 0.76% 70.07% 36ms 0.76% [libvtkCommonCore-9.3.so.9.3] 0 0% 70.07% 36ms 0.76% std::_Destroy (inline) 2ms 0.042% 70.11% 36ms 0.76% std::_Destroy_aux::__destroy (inline) 36ms 0.76% 70.86% 36ms 0.76% vtkObjectBase::~vtkObjectBase 0 0% 70.86% 35ms 0.73% vtk::detail::smp::vtkSMPToolsImplForTBB 35ms 0.73% 71.60% 35ms 0.73% vtkObjectBase::vtkObjectBase 0 0% 71.60% 34ms 0.71% Edge::SetNodes (inline) 13ms 0.27% 71.87% 34ms 0.71% __find_specmb (inline) 34ms 0.71% 72.59% 34ms 0.71% boost::numeric::ublas::c_vector::operator() 4ms 0.084% 72.67% 34ms 0.71% boost::serialization::singleton::get_instance 28ms 0.59% 73.26% 34ms 0.71% std::num_put::do_put 12ms 0.25% 73.51% 33ms 0.69% _int_free_merge_chunk 1ms 0.021% 73.53% 33ms 0.69% std::basic_filebuf::overflow 3ms 0.063% 73.59% 33ms 0.69% tbb::detail::r1::cancel_group_execution 31ms 0.65% 74.24% 32ms 0.67% __GI___libc_write 0 0% 74.24% 32ms 0.67% std::__basic_file::xsputn 0 0% 74.24% 32ms 0.67% std::basic_filebuf::_M_convert_to_external 3ms 0.063% 74.31% 32ms 0.67% vtkAOSDataArrayTemplate::InsertTuple 0 0% 74.31% 31ms 0.65% Cell::GetCellId 0 0% 74.31% 31ms 0.65% CxxTest::RealWorldDescription::setUp 0 0% 74.31% 31ms 0.65% PMPI_Init_thread 0 0% 74.31% 31ms 0.65% PetscInitialize 0 0% 74.31% 31ms 0.65% PetscSetup::setUpWorld 0 0% 74.31% 31ms 0.65% PetscSetupUtils::CommonSetup 0 0% 74.31% 31ms 0.65% PetscSetupUtils::InitialisePetsc 0 0% 74.31% 31ms 0.65% ompi_mpi_init 0 0% 74.31% 31ms 0.65% std::less::operator() (inline) 31ms 0.65% 74.96% 31ms 0.65% std::operator< (inline) 1ms 0.021% 74.98% 31ms 0.65% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 74.98% 30ms 0.63% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 74.98% 30ms 0.63% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 30ms 0.63% 75.61% 30ms 0.63% vtkObject::~vtkObject 0 0% 75.61% 29ms 0.61% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 75.61% 29ms 0.61% CellIdWriter::GetCellDataForVtkOutput 0 0% 75.61% 29ms 0.61% DistributedBoxCollection::~DistributedBoxCollection 0 0% 75.61% 28ms 0.59% PottsBasedCellPopulation::AcceptCellWriter 28ms 0.59% 76.20% 28ms 0.59% std::_Rb_tree_increment 1ms 0.021% 76.22% 27ms 0.57% VtkMeshWriter::MakeVtkMesh 26ms 0.55% 76.76% 27ms 0.57% vtkObject::ObjectFinalize 0 0% 76.76% 26ms 0.55% 19ms 0.4% 77.16% 26ms 0.55% AbstractMesh::GetNode 26ms 0.55% 77.71% 26ms 0.55% [libstdc++.so.6.0.33] 26ms 0.55% 78.25% 26ms 0.55% __mpn_divrem 0 0% 78.25% 26ms 0.55% boost::numeric::ublas::c_vector::assign (inline) 26ms 0.55% 78.80% 26ms 0.55% std::codecvt::do_always_noconv 4ms 0.084% 78.88% 26ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 78.88% 25ms 0.52% std::vector::vector (inline) 0 0% 78.88% 25ms 0.52% vtkDataArrayPrivate::DoComputeScalarRange 3ms 0.063% 78.95% 24ms 0.5% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 78.95% 24ms 0.5% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 4ms 0.084% 79.03% 24ms 0.5% std::__new_allocator::construct (inline) 0 0% 79.03% 24ms 0.5% std::allocator_traits::construct (inline) 4ms 0.084% 79.11% 24ms 0.5% vtkAOSDataArrayTemplate::AllocateTuples